35 Phylogeny Flashcards
Evolution is…
genetic changes in the composition of a population including…
- emergence of species
- divergence of species
- extinction of species
Evolution involves…
variation
heredity
selection
Variation must be…
heritable so it is passed onto the next generation
Change in evolution must be…and occur in…
genetic
a population, not individual
Does the individual or gene pool evolve?
gene pool
2 step process of genetic change in a population
- genetic change occurs - ex. mutation or recombination
- different alleles increase or decrease in frequency in the gene pool
mutation causes…
new alleles
recombination causes
new combinations of alleles
diversity
different alleles are present at a locus in a population
classical hypothesis
- organisms need low levels of heterozygosity so they are well-adapted to their environment
- selection favors well adapted genotypes
- each individual should be well adapted to its environment and therefore there should be little variation
balance hypothesis
- organisms need high levels of heterozygosity so they can respond to changes in the environment
- a successful population would have lots of variability to produce a variety of phenotypes and allow adaptation to a changing environment
- there should be a lot of variability in the population
neutralist theory
- many mutations are neutral
- this causes polymorphisms
- these are maintained since neither form has an advance and mutant types are not affected by selection
Two proteins with slightly different amino acid sequences both have proper level of function
this supports…
neutralist theory
selectionist theory
many poplymorphisms are maintained in the population due to selection
two forms of protein may allow for optimum performance over a range of cellular conditions
this supports…
selectionist theory
heterozygous sickle cell where an individual has protection against malaria but does not get sickle cell supports
selectionist theory
nearly neutral model
in some cases a heterozygous condition is advantageous but most mutations are neutral
factors effecting diversity within a population
- migration
- mutation
- genetic drift
- inbreeding
- natural selection
- recombination
migration and mutation
introduces variability within populations by introducing new alleles
genetic drift
decreases diversity within populations as alleles are fixed and lost
inbreeding
increases homozygous types with decrease of heterozygous types - no change in allele frequency
natural selection
can increase or decrease variability within population depending on the type of selection
recombination
increase variability
pecies
a group of individuals that actually or potentially interbreed in nature
reproductive isolation
species become distinct when they no longer exchange genes
Why does reproductive isolation occur?
- individuals does choose to mate with each other or cannot mate with each other
- their progeny are sterile or inviable
prezygotic barriers to speciation
- occur before mating occurs
- oganisms chose not to or cannot mate with each other
postzygotic barriers to speciation
- progeny are sterile or inviable
biological species concept
members of a species are capable of inter-mating and producing fertile progeny
examples of prezygotic barriers to speciation
- ecological - differences in habitat
- temporal - reproduction takes place at different times
- mechanical - anatomical differences prevent copulation
- behavioral - differences in mating behavior
- genetic - gametes are incompatible
examples of postzygotic barriers to speciation
- hybrid inviability
- hybrid sterility
- hybrid breakdown
hybrid inviability
hybrid zygote does not survive to reproduction
hybrid sterility
hybrid is sterile
hybrid breakdown
F1 hybrids are viable and fertile but F2 are inviable or sterile
allopatric speciation
geographic barrier initiates speciation by blocking gene flow/barrier to reproduction
example of allopatric speciation
Darwin’s finches
Darwin’s Finches
- 14 species evolved from a single ancestral species
- the ancestral species migrated to the Galapaogs Islands
- as new islands were produced, birds migrated to them
- the ocean formed a geographical barrier
- over time, behavioral isolation occurred leading to differences in song type
sympatric speciation
arises within a single interbreeding population without geographical barriers to gene glow
example of sympatric speciation
races of apple maggot fly
- disruptive selection depending on resource environment
- original fly fed on hawthorn tree, mutation allowed it to feed on apples
- those with the mutation mated on apple trees leading to reproductive isolation
allopolyploidy
- hybridization leads to this
- mechanism for sympatric speciation
- 2 species mate producing sterile F1
- chromosome doubling occurs producing fertile plant with two copies of each chromosome
anagenesis
evolution within a lineage over time
cladogenesis
splitting of one lineage into two
- once occurs, the two branches evolve separately from each other
cladogenesis leads to…
biological diversity since more species exist at the same time
phylogenetics
study of the relationship among and between species, individuals, or genes/alleles based on their characteristics
constructed by inferring evolutionary relationships among present day organisms
What can be measured to evaluated evolutionary divergence
- morphology
- chromosome structure
- protein sequences
- DNA sequences
inversions suppress..
crossover since gametes produced through recombination are not viable
selection tends to favor…
the individuals who are homozygous for each allele and does not favor heterozygotes
paralogs
homologous sequences in the same species
arrive through gene duplication
orthologs
homologous sequences found in different species
compare orthologous and paralogous sequences to evaluate…
the amount of change over time between and within species
Gene duplication allows
genes to evolve different functions
ex of gene duplication
successive gene duplications occurred resulting in different chains of the immune system genes and the myoglobin gene
the highest rate of nucleotide substitution are in
sequences that have the least effect on protein function
molecular clock
the relationship between the constant mutation rate in the change of DNA/amino acid sequence and the differences in sequence between present day organisms that assumes a linear rate of mutation over time
the relative values of the rate of nucleotide substitution per site per year correlate in what way with their function
- negatively
- such that mutations that greatly affect the sequence or function of protein are less common than those that do not have such a large effect on protein function
the lowest number of nucleotide substitutions occur as…
the nonsynonymous changes
they are rate
the highest number of changes that occur are…
synonomous changes
the promoter is in the…
5’ flanking
pseudogenes
areas of the DNA that do not code for functional genes but have similar sequences to the function genes
produced by gene duplication and accumulate mutations without causing a disruption in normal function
operational taxonomic units
can be a species or a strain of a virus or different alleles within a species
examined in phylogenetic trees to show the degrees of similarity
rooted tree
have common ancestor for all terminal nodes
the distance between OTUS is known and the order of divergence is inferred by comparing to an OTU that is an outgroup
outgroup
an OTU that is known to have diverged earlier than all of the other OTUs
unrooted trees
do not have a common ancestor
only the distance between OTUs is known not the order of divergence
terminal nodes
the nodes at the end of the tree
internal nodes
nodes located within the middle of the tree
DNA sequence alignment
identification of homolgous genes and properly aligning their sequence to determine an accurate tree
distance approach
- computing difference to infer relationships based on overall similarity of organisms by typically using multiple phenotypic characterisistics or gene sequence
UPGMA
unweighted pair group method with arithmetic mean
method of constructing a phylogenetic tree based on computing difference in DNA sequences
